[gmx-users] mdp-settings for charmm36 and lipid apl values

Gmx QA gmxquestions at gmail.com
Wed May 8 17:09:06 CEST 2013

Hi gmx-users,

I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input nonetheless :-)

The relevant sections of my mdp-file are pasted below:

; Start time and timestep in ps
tinit                    = 0
dt                       = 0.001
nsteps                   = 100000000

; nblist update frequency
nstlist                  = 5
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic_molecules       = no
; nblist cut-off
rlist                    = 1.2
; long-range cut-off for switched potentials
rlistlong                = 1.4

; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = switch
; cut-off lengths
rvdw-switch              = 0.8
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No

; Temperature coupling
tcoupl                   = V-rescale
nsttcouple               = -1
nh-chain-length          = 10
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 300
; Pressure coupling
pcoupl                   = Parrinello-Rahman
pcoupltype               = semiisotropic
nstpcouple               = -1

This is as far as I can tell from earlier discussions on the list, and also
from reading the Piggott et al. paper in JCTC, the correct settings for

After a simulation of ~50 ns, I use GridMatMD to calculate the area per
headgroup of POPC and POPE, respectively, and get what I think are not 100%
acceptable results (but maybe they are)

For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.

The value for POPE would have been fine I suppose if it hadn't been for the
fact that the APL for POPC is smaller. Should it not be larger than POPE?

I notice in the Piggott-paper that they in the supplement for some
simulations of POPC also get APL's of around 59-60 (without POPE of
course), and that the results depend to some extent also on the usage of
TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here.

Could anyone comment on (a) my mdp-file settings, and (b) the resulting
APL, and tell me if I should be worried about anything?


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